Regarding the character designs, we have stated on multiple occasions that these are subject to change. In addition, the reason Kouya doesn't wink is because we haven't provided that image yet. As far as the code goes, Kouya does have calls for a winking sprite, but for the moment, the image it uses is just his smiling sprite. Again, this is just temporary until we get additional sprite work done.
With Kyouji, we decided we wanted to keep his eyes similar to the original for one main reason. In Japan, "fox eyes" is a common trope used to identify when a character is very wise and reliable. Both of these are intrinsic qualities for Kyouji, and so, it was deemed appropriate to keep them like that.
The aging up of characters was done for one major reason: legality. While the national age of consent in Japan is 13, all prefectures have overridden this with their own age, most of which are around 17-18. While the original team could have gotten away with having sexual interaction with a 16 year old (who acts like an 8 year old), we won't. Not to mention, Soutarou was originally the youngest at 15, so yeah...there's that too. Now, Shun is the youngest of the group, even if he is 18, because he was the last to have his 18th birthday.
Finally, Hiroyuki: Originally, he was a self-insert, but therein lies the problem. Self-inserts are notoriously difficult to write for, especially for consistency purposes. The original game, as much as all of us in Stormsinger Studios enjoyed it, suffers from an extreme level of inconsistencies, especially where Hiroyuki is concerned. To remedy this, it was felt that making him have a specific personality and removing the self-insert aspects would be best. We have mentioned multiple times in the past about why we removed humans entirely. You can see this in the FAQ (which does admittedly need updating a bit).